
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()

os.chdir(data_dir.name)


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Make sure that the version used is the right one

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.8.2
Using NPTT version:  2.0.1


testing_data = {                
               
                'ifu_g395h_f290lp':{
                                  'uncal_file_nrs1': 'ifu_g395h_f290lp_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'ifu_g395h_f290lp_nrs2_uncal.fits',
                                  'truth_file_nrs1': 'ifu_g395h_f290lp_nrs1_assign_wcs_truth.fits',
                                  'truth_file_nrs2': 'ifu_g395h_f290lp_nrs2_assign_wcs_truth.fits',
                                  'msa_shutter_config': None }

               }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'truth_file_nrs1', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# Set common NPTT switches for this test and run the test for both detectors for each data set

# define benchmark (or 'truth') file
compare_assign_wcs_and_extract_2d_with_esa = False

# accepted threshold difference with respect to benchmark files
threshold_diff = 1e-7

# other variables
esa_files_path, raw_data_root_file = None, None
save_figs = False
show_figs = True
detectors = ['nrs1', 'nrs2']
results_dict = {}


# Test the IFU data
for mode_config, data_set_dict in testing_data.items():
    if 'ifu' not in mode_config:
        continue
        
    print('IFU mode:  ', mode_config)
    for det in detectors:
        print('Testing files for detector: ', det)
        data = get_artifactory_file(data_set_dict, det)
        uncal_file, truth_file, msa_shutter_config = data
        uncal_basename = os.path.basename(uncal_file)
        print('Working with uncal_file: ', uncal_basename)
        
        # Make sure that there is an assign_wcs truth product to compare to, else skip this data set
        if truth_file is None:
            print('No truth file to compare to for this detector, skipping this data set.  \n')
            skip_file = True
        
        # Make sure these keywords are properly set
        filt = fits.getval(uncal_file, 'FILTER')
        if 'OPAQUE' in filt:
            if 'clear' in uncal_basename.lower():
                filt = 'CLEAR'
            else:
                l = uncal_basename.split("_")
                for li in l:
                    if 'lp' in li:
                        filt = li.upper()
                        break
            fits.setval(uncal_file, 'FILTER', value=filt)
        print('Filter = ', filt)

        # Run the stage 1 pipeline 
        print('Running detector1 pipeline...')
        rate_object = Detector1Pipeline.call(uncal_file)
        
        # Run the stage 2 pipeline steps
        print('Running spec2 pipeline')
        try:
            assign_wcs_object = AssignWcsStep.call(rate_object)
            skip_file = False
        except:
            print("No open slits fall on detector ", det)
            print("Skipping test for this file. \n")
            skip_file = True
            
        if not skip_file:  
            # Run the validation test
            %matplotlib inline
            print('Running test for IFU...')
            result, _ = nptt.calwebb_spec2_pytests.auxiliary_code.compare_wcs_ifu.compare_wcs(
                                                                            assign_wcs_object, 
                                                                            truth_file=truth_file, 
                                                                            esa_files_path=esa_files_path, 
                                                                            show_figs=show_figs,
                                                                            save_figs=save_figs, 
                                                                            threshold_diff=threshold_diff, 
                                                                            raw_data_root_file=raw_data_root_file)
        else:
            result = 'skipped'

        # Did the test passed 
        print("Did IFU assign_wcs validation test passed? ", result, "\n\n")
        rd = {uncal_basename: result}
        results_dict.update(rd)

IFU mode:   ifu_g395h_f290lp
Testing files for detector:  nrs1
Working with uncal_file:  ifu_g395h_f290lp_nrs1_uncal.fits
Filter =  F290LP
Running detector1 pipeline...

2022-12-02 15:03:41,283 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-12-02 15:03:41,309 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-12-02 15:03:41,311 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-12-02 15:03:41,313 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-12-02 15:03:41,314 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-12-02 15:03:41,315 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-12-02 15:03:41,316 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-12-02 15:03:41,317 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-12-02 15:03:41,318 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-12-02 15:03:41,319 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-12-02 15:03:41,321 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-12-02 15:03:41,322 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-12-02 15:03:41,323 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-12-02 15:03:41,324 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-12-02 15:03:41,325 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-12-02 15:03:41,327 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-12-02 15:03:41,328 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-12-02 15:03:41,330 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-12-02 15:03:41,557 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq/ifu_g395h_f290lp_nrs1_uncal.fits',).
2022-12-02 15:03:41,568 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-12-02 15:03:41,986 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_g395h_f290lp_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-12-02 15:03:42,001 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits'.
2022-12-02 15:03:42,003 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits'.
2022-12-02 15:03:42,005 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits'.
2022-12-02 15:03:42,006 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits'.
2022-12-02 15:03:42,008 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-12-02 15:03:42,009 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits'.
2022-12-02 15:03:42,010 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits'.
2022-12-02 15:03:42,012 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-12-02 15:03:42,013 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-12-02 15:03:42,014 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0031.fits'.
2022-12-02 15:03:42,015 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits'.
2022-12-02 15:03:42,017 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-12-02 15:03:42,017 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-12-02 15:03:42,018 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-12-02 15:03:43,148 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:43,150 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:03:44,000 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-12-02 15:03:44,002 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-12-02 15:03:44,006 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-12-02 15:03:44,170 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:44,172 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:03:44,198 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0010.fits
2022-12-02 15:03:45,642 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-12-02 15:03:45,816 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:45,818 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq', 'n_pix_grow_sat': 1}
2022-12-02 15:03:45,844 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0031.fits
2022-12-02 15:03:51,290 - stpipe.Detector1Pipeline.saturation - INFO - Detected 176585 saturated pixels
2022-12-02 15:03:51,447 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-12-02 15:03:51,479 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-12-02 15:03:51,636 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:51,638 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:03:51,638 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-12-02 15:03:51,641 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-12-02 15:03:51,752 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:51,753 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:03:51,779 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0117.fits
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stdatamodels/validate.py:38: ValidationWarning: While validating meta.exposure.readpatt the following error occurred:
'ALLIRS2' is not one of ['ACQ1', 'ACQ2', 'BRIGHT1', 'BRIGHT2', 'DEEP2', 'DEEP8', 'FAST', 'FASTGRPAVG', 'FASTGRPAVG8', 'FASTGRPAVG16', 'FASTGRPAVG32', 'FASTGRPAVG64', 'FASTR1', 'FASTR100', 'FGS', 'FGS60', 'FGS8370', 'FGS840', 'FGSRAPID', 'FINEGUIDE', 'ID', 'MEDIUM2', 'MEDIUM8', 'NIS', 'NISRAPID', 'NRS', 'NRSIRS2', 'NRSN16R4', 'NRSN32R8', 'NRSN8R2', 'NRSRAPID', 'NRSIRS2RAPID', 'NRSRAPIDD1', 'NRSRAPIDD2', 'NRSRAPIDD6', 'NRSSLOW', 'RAPID', 'SHALLOW2', 'SHALLOW4', 'SLOW', 'SLOWR1', 'TRACK', 'ANY', 'N/A']

Failed validating 'enum' in schema:
    OrderedDict([('title', 'Readout pattern'),
                 ('type', 'string'),
                 ('enum',
                  ['ACQ1',
                   'ACQ2',
                   'BRIGHT1',
                   'BRIGHT2',
                   'DEEP2',
                   'DEEP8',
                   'FAST',
                   'FASTGRPAVG',
                   'FASTGRPAVG8',
                   'FASTGRPAVG16',
                   'FASTGRPAVG32',
                   'FASTGRPAVG64',
                   'FASTR1',
                   'FASTR100',
                   'FGS',
                   'FGS60',
                   'FGS8370',
                   'FGS840',
                   'FGSRAPID',
                   'FINEGUIDE',
                   'ID',
                   'MEDIUM2',
                   'MEDIUM8',
                   'NIS',
                   'NISRAPID',
                   'NRS',
                   'NRSIRS2',
                   'NRSN16R4',
                   'NRSN32R8',
                   'NRSN8R2',
                   'NRSRAPID',
                   'NRSIRS2RAPID',
                   'NRSRAPIDD1',
                   'NRSRAPIDD2',
                   'NRSRAPIDD6',
                   'NRSSLOW',
                   'RAPID',
                   'SHALLOW2',
                   'SHALLOW4',
                   'SLOW',
                   'SLOWR1',
                   'TRACK',
                   'ANY',
                   'N/A']),
                 ('fits_ke ...
  warnings.warn(errmsg, ValidationWarning)
2022-12-02 15:03:53,535 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-12-02 15:03:53,668 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:03:53,670 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-12-02 15:03:53,696 - stpipe.Detector1Pipeline.refpix - INFO - Using refpix reference file: /grp/crds/cache/references/jwst/jwst_nirspec_refpix_0019.fits
2022-12-02 15:03:55,765 - stpipe.Detector1Pipeline.refpix - INFO - Working on integration 1
2022-12-02 15:05:11,906 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-12-02 15:05:12,131 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:05:12,133 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:05:12,163 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0022.fits
2022-12-02 15:05:13,012 - stpipe.Detector1Pipeline.linearity - WARNING - Keyword BAD_LIN_CORR does not correspond to an existing DQ mnemonic, so will be ignored
2022-12-02 15:05:14,809 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-12-02 15:05:14,928 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:05:14,930 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq', 'dark_output': None}
2022-12-02 15:05:15,255 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0088.fits
2022-12-02 15:05:50,728 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=20, nframes=1, groupgap=0
2022-12-02 15:05:50,729 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=65, nframes=1, groupgap=0
2022-12-02 15:05:52,327 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-12-02 15:05:52,471 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:05:52,473 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}
2022-12-02 15:05:52,681 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-12-02 15:05:52,929 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2022-12-02 15:05:53,286 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-12-02 15:05:54,324 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-12-02 15:05:54,512 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-12-02 15:06:02,597 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 65989 pixels with at least one CR from five or more groups.
2022-12-02 15:06:23,690 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 29.3655 sec
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:302: RuntimeWarning: invalid value encountered in divide
  data /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:303: RuntimeWarning: invalid value encountered in divide
  err /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:304: RuntimeWarning: invalid value encountered in divide
  readnoise_2d /= gain_2d
2022-12-02 15:06:24,045 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 31.363607
2022-12-02 15:06:24,052 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-12-02 15:06:24,218 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 20, 3200, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:06:24,220 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-12-02 15:06:24,633 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0018.fits
2022-12-02 15:06:24,634 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0023.fits
2022-12-02 15:06:24,730 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-12-02 15:06:24,731 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-12-02 15:09:16,562 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 20
2022-12-02 15:09:16,563 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-12-02 15:09:16,778 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-12-02 15:09:16,932 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:09:16,934 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:09:16,993 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2022-12-02 15:09:17,011 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-02 15:09:17,137 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:09:17,139 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq'}
2022-12-02 15:09:17,201 - stpipe.Detector1Pipeline.gain_scale - INFO - Rescaling by 1.0
2022-12-02 15:09:17,219 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-02 15:09:17,220 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-12-02 15:09:17,221 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-02 15:09:17,221 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-12-02 15:09:17,233 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-02 15:09:17,348 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_g395h_f290lp_nrs1_uncal.fits>,).
2022-12-02 15:09:17,350 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}

Running spec2 pipeline

2022-12-02 15:09:17,570 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.1448970586061478 deg
2022-12-02 15:09:17,571 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3232757747173309 deg
2022-12-02 15:09:17,571 - stpipe.AssignWcsStep - INFO - theta_y correction: -3.766823889842878e-13 deg
2022-12-02 15:09:17,573 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-02 15:09:21,055 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0005.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0035.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0022.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
2022-12-02 15:09:28,483 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS  156.176999392 -45.687618156 156.178775679 -45.687618156 156.178775679 -45.686331563 156.176999392 -45.686331563
2022-12-02 15:09:28,485 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2022-12-02 15:09:28,499 - stpipe.AssignWcsStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-02 15:09:28,500 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done

Running test for IFU...
Information from the 'truth' (or comparison) file 
Filename: /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq/ifu_g395h_f290lp_nrs1_assign_wcs_truth.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     291   ()      
  1  SCI           1 ImageHDU        50   (2048, 2048)   float32   
  2  ERR           1 ImageHDU        10   (2048, 2048)   float32   
  3  DQ            1 ImageHDU        11   (2048, 2048)   int32 (rescales to uint32)   
  4  VAR_POISSON    1 ImageHDU         9   (2048, 2048)   float32   
  5  VAR_RNOISE    1 ImageHDU         9   (2048, 2048)   float32   
  6  ASDF          1 BinTableHDU     11   1R x 1C   [1637418B]   
None
Comparing to ST 'truth' file.
from assign_wcs file  -->     Detector: NRS1   Grating: G395H   Filter: F290LP   Lamp: REF
GWA_XTILT: 0.3232757747173309
GWA_YTILT: 0.1448970586061478
GWA_TTILT: 37.16754109485964

 Working with slice: 00
Avalable frames:  ['detector', 'sca', 'gwa', 'slit_frame', 'slicer', 'msa_frame', 'oteip', 'v2v3', 'v2v3vacorr', 'world']

   Relative Wavelength Difference  :   mean = 7.573e-16    median = 0.000e+00    stdev = 1.242e-13
    Maximum   RelativeWavelength Difference = 2.088e-11
    Minimum   RelativeWavelength Difference = -7.439e-12
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeWavelength Difference = 2.088e-11
    Minimum   RelativeWavelength Difference = -7.439e-12
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

   Relative Slit-Y Difference  :   mean = 6.392e-16    median = 0.000e+00    stdev = 8.506e-15
    Maximum   RelativeSlit-Y Difference = 2.376e-13
    Minimum   RelativeSlit-Y Difference = -0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeSlit-Y Difference = 2.376e-13
    Minimum   RelativeSlit-Y Difference = -0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

   Relative MSA_X Difference  :   mean = 9.540e-21    median = 0.000e+00    stdev = 1.266e-18
    Maximum   RelativeMSA_X Difference = 1.680e-16
    Minimum   RelativeMSA_X Difference = 0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeMSA_X Difference = 1.680e-16
    Minimum   RelativeMSA_X Difference = 0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

   Relative MSA_Y Difference  :   mean = 6.390e-16    median = 0.000e+00    stdev = 8.503e-15
    Maximum   RelativeMSA_Y Difference = 2.377e-13
    Minimum   RelativeMSA_Y Difference = -0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeMSA_Y Difference = 2.377e-13
    Minimum   RelativeMSA_Y Difference = -0.000e+00
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

   Relative V2 difference  :   mean = -5.291e-19    median = 0.000e+00    stdev = 1.777e-17
    Maximum   RelativeV2 difference = 5.691e-16
    Minimum   RelativeV2 difference = -1.706e-15
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeV2 difference = 5.691e-16
    Minimum   RelativeV2 difference = -1.706e-15
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%

   Relative V3 difference  :   mean = -2.817e-19    median = 0.000e+00    stdev = 1.228e-17
    Maximum   RelativeV3 difference = 2.277e-16
    Minimum   RelativeV3 difference = -4.567e-16
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
    Maximum   RelativeV3 difference = 2.277e-16
    Minimum   RelativeV3 difference = -4.567e-16
    Percentage of pixels where median of relative differences is greater than: 
                            ->  1xtheshold = 0%
                            ->  3xtheshold = 0%
                            ->  5xtheshold = 0%
No output_directory was provided. Figures will be saved in current working directory:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmpk1odjljq/00_NRS1_rel_wave_diffs.png

No output_directory was provided. Figures will NOT be saved.

No output_directory was provided. Figures will NOT be saved.

No output_directory was provided. Figures will NOT be saved.

No output_directory was provided. Figures will NOT be saved.

No output_directory was provided. Figures will NOT be saved.


# Summary of modes tested and their results 

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<42} {:<8}'.format(key, val))

These are the final results of the tests: 
ifu_g395h_f290lp_nrs1_uncal.fits           PASSED  
ifu_g395h_f290lp_nrs2_uncal.fits           PASSED

JWST Pipeline Validation Testing Notebook: NIRSpec, spec2, assign_wcs step for ifu¶

Table of Contents¶

Imports¶

Test Description¶

Results¶

Calibration WG Requested Algorithm:¶

Defining Term¶

Run the JWST pipeline and assign_wcs validation tests¶

Testing Data Set¶

About this Notebook¶